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oestebanoesteban
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fix: Dockerfile fails to build bc of ubuntu deprecations
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‎Dockerfile‎

Lines changed: 90 additions & 175 deletions
Original file line numberDiff line numberDiff line change
@@ -2,7 +2,7 @@
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#
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# MIT License
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#
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# Copyright (c) 2021 The NiPreps Developers
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# Copyright (c) 2022 The NiPreps Developers
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#
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# Permission is hereby granted, free of charge, to any person obtaining a copy
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# of this software and associated documentation files (the "Software"), to deal
@@ -22,29 +22,10 @@
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# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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# SOFTWARE.
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# Use Ubuntu 20.04 LTS
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FROM ubuntu:focal-20210416
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FROM nipreps/miniconda:py38_1.4.2
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# Prepare environment
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RUN apt-get update && \
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apt-get install -y --no-install-recommends \
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apt-utils \
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autoconf \
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build-essential \
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bzip2 \
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ca-certificates \
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curl \
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git \
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libtool \
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lsb-release \
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pkg-config \
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unzip \
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xvfb && \
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apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
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ENV DEBIAN_FRONTEND="noninteractive" \
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LANG="en_US.UTF-8" \
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LC_ALL="en_US.UTF-8"
27+
ARG DEBIAN_FRONTEND=noninteractive
28+
ENV LD_LIBRARY_PATH="/usr/lib/x86_64-linux-gnu:${CONDA_PATH}/lib"
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# Installing freesurfer
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RUN curl -sSL https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.1/freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1.tar.gz | tar zxv --no-same-owner -C /opt \
@@ -69,7 +50,7 @@ RUN curl -sSL https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.1/frees
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--exclude='freesurfer/trctrain'
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# Simulate SetUpFreeSurfer.sh
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ENV FSL_DIR="/opt/fsl-6.0.5.1" \
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ENV FSL_DIR="/opt/fsl" \
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OS="Linux" \
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FS_OVERRIDE=0 \
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FIX_VERTEX_AREA="" \
@@ -86,86 +67,98 @@ ENV PERL5LIB="$MINC_LIB_DIR/perl5/5.8.5" \
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MNI_PERL5LIB="$MINC_LIB_DIR/perl5/5.8.5" \
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PATH="$FREESURFER_HOME/bin:$FSFAST_HOME/bin:$FREESURFER_HOME/tktools:$MINC_BIN_DIR:$PATH"
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70+
# Install AFNI latest (neurodocker build)
71+
ENV AFNI_DIR="/opt/afni"
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RUN echo "Downloading AFNI ..." \
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&& mkdir -p ${AFNI_DIR} \
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&& curl -fsSL --retry 5 https://afni.nimh.nih.gov/pub/dist/tgz/linux_openmp_64.tgz \
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| tar -xz -C ${AFNI_DIR} --strip-components 1 \
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# Keep only what we use
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&& find ${AFNI_DIR} -type f -not \( \
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-name "3dTshift" -or \
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-name "3dUnifize" -or \
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-name "3dAutomask" -or \
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-name "3dvolreg" \) -delete
82+
83+
ENV PATH="${AFNI_DIR}:$PATH" \
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AFNI_IMSAVE_WARNINGS="NO" \
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AFNI_MODELPATH="${AFNI_DIR}/models" \
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AFNI_TTATLAS_DATASET="${AFNI_DIR}/atlases" \
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AFNI_PLUGINPATH="${AFNI_DIR}/plugins"
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89+
# Install AFNI's dependencies
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RUN ${CONDA_PATH}/bin/conda install -c conda-forge -c anaconda \
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gsl \
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xorg-libxp \
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scipy=1.8 \
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&& ${CONDA_PATH}/bin/conda install -c sssdgc png \
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&& sync \
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&& ${CONDA_PATH}/bin/conda clean -afy; sync \
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&& rm -rf ~/.conda ~/.cache/pip/*; sync \
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&& ln -s ${CONDA_PATH}/lib/libgsl.so.25 /usr/lib/x86_64-linux-gnu/libgsl.so.19 \
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&& ln -s ${CONDA_PATH}/lib/libgsl.so.25 /usr/lib/x86_64-linux-gnu/libgsl.so.0 \
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&& ldconfig
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RUN apt-get update \
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&& apt-get install -y -q --no-install-recommends \
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libcurl4-openssl-dev \
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libgdal-dev \
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libgfortran-8-dev \
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libgfortran4 \
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libglw1-mesa \
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libgomp1 \
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libjpeg62 \
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libnode-dev \
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libssl-dev \
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libudunits2-dev \
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libxm4 \
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libxml2-dev \
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netpbm \
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tcsh \
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xfonts-base \
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&& apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* \
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&& ldconfig
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# Installing ANTs 2.3.4 (NeuroDocker build)
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ENV ANTSPATH="/opt/ants"
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WORKDIR $ANTSPATH
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RUN curl -sSL "https://dl.dropbox.com/s/gwf51ykkk5bifyj/ants-Linux-centos6_x86_64-v2.3.4.tar.gz" \
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| tar -xzC $ANTSPATH --strip-components 1
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ENV PATH="$ANTSPATH:$PATH"
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# FSL 6.0.5.1
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RUN apt-get update -qq \
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&& apt-get install -y -q --no-install-recommends \
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bc \
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dc \
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file \
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libfontconfig1 \
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libfreetype6 \
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libgl1-mesa-dev \
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libgl1-mesa-dri \
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libglu1-mesa-dev \
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libgomp1 \
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libice6 \
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libxcursor1 \
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libxft2 \
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libxinerama1 \
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libxrandr2 \
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libxrender1 \
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libxt6 \
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sudo \
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wget \
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&& apt-get clean \
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&& rm -rf /var/lib/apt/lists/* \
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&& echo "Downloading FSL ..." \
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&& mkdir -p /opt/fsl-6.0.5.1 \
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&& curl -fsSL --retry 5 https://fsl.fmrib.ox.ac.uk/fsldownloads/fsl-6.0.5.1-centos7_64.tar.gz \
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| tar -xz -C /opt/fsl-6.0.5.1 --strip-components 1 \
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--exclude "fsl/config" \
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--exclude "fsl/data/atlases" \
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--exclude "fsl/data/first" \
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--exclude "fsl/data/mist" \
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--exclude "fsl/data/possum" \
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--exclude "fsl/data/standard/bianca" \
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--exclude "fsl/data/standard/tissuepriors" \
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--exclude "fsl/doc" \
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--exclude "fsl/etc/default_flobs.flobs" \
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--exclude "fsl/etc/fslconf" \
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--exclude "fsl/etc/js" \
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--exclude "fsl/etc/luts" \
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--exclude "fsl/etc/matlab" \
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--exclude "fsl/extras" \
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--exclude "fsl/include" \
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--exclude "fsl/python" \
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--exclude "fsl/refdoc" \
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--exclude "fsl/src" \
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--exclude "fsl/tcl" \
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--exclude "fsl/bin/FSLeyes" \
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&& find /opt/fsl-6.0.5.1/bin -type f -not \( \
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-name "applywarp" -or \
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-name "bet" -or \
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-name "bet2" -or \
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-name "convert_xfm" -or \
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-name "fast" -or \
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-name "flirt" -or \
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-name "fsl_regfilt" -or \
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-name "fslhd" -or \
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-name "fslinfo" -or \
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-name "fslmaths" -or \
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-name "fslmerge" -or \
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-name "fslroi" -or \
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-name "fslsplit" -or \
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-name "fslstats" -or \
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-name "imtest" -or \
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-name "mcflirt" -or \
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-name "melodic" -or \
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-name "prelude" -or \
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-name "remove_ext" -or \
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-name "susan" -or \
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-name "topup" -or \
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-name "zeropad" \) -delete \
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&& find /opt/fsl-6.0.5.1/data/standard -type f -not -name "MNI152_T1_2mm_brain.nii.gz" -delete
160-
ENV FSLDIR="/opt/fsl-6.0.5.1" \
161-
PATH="/opt/fsl-6.0.5.1/bin:$PATH" \
130+
RUN curl -sSL https://fsl.fmrib.ox.ac.uk/fsldownloads/fsl-6.0.5.1-centos7_64.tar.gz | tar zxv --no-same-owner -C /opt \
131+
--exclude='fsl/doc' \
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--exclude='fsl/refdoc' \
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--exclude='fsl/python/oxford_asl' \
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--exclude='fsl/data/possum' \
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--exclude='fsl/data/first' \
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--exclude='fsl/data/mist' \
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--exclude='fsl/data/atlases' \
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--exclude='fsl/data/xtract_data' \
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--exclude='fsl/extras/doc' \
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--exclude='fsl/extras/man' \
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--exclude='fsl/extras/src' \
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--exclude='fsl/src' \
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--exclude='fsl/tcl'
144+
145+
ENV FSLDIR="/opt/fsl" \
146+
PATH="/opt/fsl/bin:$PATH" \
162147
FSLOUTPUTTYPE="NIFTI_GZ" \
163148
FSLMULTIFILEQUIT="TRUE" \
149+
FSLTCLSH="/opt/fsl/bin/fsltclsh" \
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FSLWISH="/opt/fsl/bin/fslwish" \
164151
FSLLOCKDIR="" \
165152
FSLMACHINELIST="" \
166153
FSLREMOTECALL="" \
167154
FSLGECUDAQ="cuda.q" \
168-
LD_LIBRARY_PATH="/opt/fsl-6.0.5.1/lib:$LD_LIBRARY_PATH"
155+
POSSUMDIR="/opt/fsl" \
156+
LD_LIBRARY_PATH="${LD_LIBRARY_PATH}:/opt/fsl"
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158+
# Unless otherwise specified each process should only use one thread - nipype
159+
# will handle parallelization
160+
ENV MKL_NUM_THREADS=1 \
161+
OMP_NUM_THREADS=1
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170163
# Convert3D (neurodocker build)
171164
RUN echo "Downloading Convert3D ..." \
@@ -178,84 +171,6 @@ RUN echo "Downloading Convert3D ..." \
178171
ENV C3DPATH="/opt/convert3d-1.0.0" \
179172
PATH="/opt/convert3d-1.0.0/bin:$PATH"
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# AFNI latest (neurodocker build)
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RUN apt-get update -qq \
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&& apt-get install -y -q --no-install-recommends \
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apt-utils \
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ed \
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gsl-bin \
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libglib2.0-0 \
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libglu1-mesa-dev \
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libglw1-mesa \
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libgomp1 \
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libjpeg62 \
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libxm4 \
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netpbm \
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tcsh \
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xfonts-base \
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xvfb \
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&& apt-get clean \
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&& rm -rf /var/lib/apt/lists/* \
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&& curl -sSL --retry 5 -o /tmp/multiarch.deb http://archive.ubuntu.com/ubuntu/pool/main/g/glibc/multiarch-support_2.27-3ubuntu1.2_amd64.deb \
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&& dpkg -i /tmp/multiarch.deb \
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&& rm /tmp/multiarch.deb \
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&& curl -sSL --retry 5 -o /tmp/libxp6.deb http://mirrors.kernel.org/debian/pool/main/libx/libxp/libxp6_1.0.2-2_amd64.deb \
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&& dpkg -i /tmp/libxp6.deb \
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&& rm /tmp/libxp6.deb \
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&& curl -sSL --retry 5 -o /tmp/libpng.deb http://snapshot.debian.org/archive/debian-security/20160113T213056Z/pool/updates/main/libp/libpng/libpng12-0_1.2.49-1%2Bdeb7u2_amd64.deb \
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&& dpkg -i /tmp/libpng.deb \
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&& rm /tmp/libpng.deb \
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&& apt-get install -f \
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&& apt-get clean \
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&& rm -rf /var/lib/apt/lists/* \
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&& gsl2_path="$(find / -name 'libgsl.so.19' || printf '')" \
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&& if [ -n "$gsl2_path" ]; then \
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ln -sfv "$gsl2_path" "$(dirname $gsl2_path)/libgsl.so.0"; \
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fi \
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&& ldconfig \
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&& echo "Downloading AFNI ..." \
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&& mkdir -p /opt/afni-latest \
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&& curl -fsSL --retry 5 https://afni.nimh.nih.gov/pub/dist/tgz/linux_openmp_64.tgz \
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| tar -xz -C /opt/afni-latest --strip-components 1 \
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--exclude "linux_openmp_64/*.gz" \
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--exclude "linux_openmp_64/funstuff" \
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--exclude "linux_openmp_64/shiny" \
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--exclude "linux_openmp_64/afnipy" \
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--exclude "linux_openmp_64/lib/RetroTS" \
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--exclude "linux_openmp_64/meica.libs" \
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# Keep only what we use
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&& find /opt/afni-latest -type f -not \( \
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-name "3dTshift" -or \
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-name "3dUnifize" -or \
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-name "3dAutomask" -or \
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-name "3dvolreg" \) -delete
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ENV PATH="/opt/afni-latest:$PATH" \
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AFNI_IMSAVE_WARNINGS="NO" \
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AFNI_PLUGINPATH="/opt/afni-latest"
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# Installing ANTs 2.3.3 (NeuroDocker build)
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# Note: the URL says 2.3.4 but it is actually 2.3.3
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ENV ANTSPATH="/opt/ants" \
240-
PATH="/opt/ants:$PATH"
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WORKDIR $ANTSPATH
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RUN curl -sSL "https://dl.dropbox.com/s/gwf51ykkk5bifyj/ants-Linux-centos6_x86_64-v2.3.4.tar.gz" \
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| tar -xzC $ANTSPATH --strip-components 1
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COPY --from=nipreps/miniconda:py38_1.3.2 /opt/conda /opt/conda
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RUN ln -s /opt/conda/etc/profile.d/conda.sh /etc/profile.d/conda.sh && \
248-
echo ". /opt/conda/etc/profile.d/conda.sh" >> ~/.bashrc && \
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echo "conda activate base" >> ~/.bashrc
250-
251-
# Set CPATH for packages relying on compiled libs (e.g. indexed_gzip)
252-
ENV PATH="/opt/conda/bin:$PATH" \
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CPATH="/opt/conda/include:$CPATH" \
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LD_LIBRARY_PATH="/opt/conda/lib:$LD_LIBRARY_PATH" \
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LANG="C.UTF-8" \
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LC_ALL="C.UTF-8" \
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PYTHONNOUSERSITE=1
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# Create a shared $HOME directory
260175
RUN useradd -m -s /bin/bash -G users niworkflows
261176
WORKDIR /home/niworkflows

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